The batteries in my 2000 Ez-Go (36V) will not hold a charge. I put them on the charger and when the charger stops its charging cycle, the battery indicator shows a full charge. If I plug the charger back in, its starts charging again.

Is this an indicator that I need new batteries?

Today

BGW

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No, all older ferroresonant EZGO chargers start at full and scale themselves back.
Get a digital meter and check your pack voltage and individual battery voltages.
The pack should be at least 38.2v and each battery should be at least 6.37v.

Thanks for the info. Finally got a DVM and my total voltage is 37.3, with two batteries having less voltage than the other four. One battery tests out at 6.03 with one cell that measures 1100 on a hydrometer with the other cells at 1250 and the other battery tests out at 6.21 with one cell at 1200 and the other cells at 1250.

Since the batteries are 3 years old, should I replace the bad batteries or replace all six?

It's always best to replace all batteries at the same time.
IMO, batteries should last from 5-7 years, 3 year old batteries should be OK but yours seem to have not been taken care of.
If you buy new ones, charging and maintenance is the key.